Name: Patrick Boyle
Location: Boston, MA
Occupation: Head of Codebase, Ginkgo BioWorks
How does someone from a remote Alaskan village end up bioengineering alternative proteins for plant-based foods? The answer lies in the experience of relying on monthly shipments of fruits and vegetables flown in from the contiguous U.S., which leaves a lasting impact. Patrick Boyle, a child of two educators dedicated to promoting educational equity in indigenous communities, relocated with his family to a small Alaskan town. Today, he serves as the Head of Codebase at Ginkgo Bioworks, a Boston-based synthetic biology company that engineers and sells organisms. Ginkgo’s Codebase encompasses thousands of innovative strains, enzymes, genetic components, and a vast array of genetic repositories, including millions of engineered DNA sequences. Their technology assists food brands in developing animal-free proteins.
Ginkgo collaborates with food brands such as EVO to create animal-free eggs through precision fermentation and works with Phytolon on natural colors. Boyle recently shared insights with Food Dive regarding his work and the future direction of the industry.
PATRICK BOYLE: “The definition of a ‘job’ can vary. If we’re talking about a full-time position with a 401k, this is my first and only real job. I held some odd jobs during high school and interned in college, and I even had a summer gig in a restaurant, which was enjoyable. I grew up in a tiny village in Alaska, but we moved to a larger town when I reached high school. That summer, I worked washing dishes and doing prep work in a brew pub, which remains my sole experience in food service.”
BOYLE: “My role involves determining how Ginkgo BioWorks can assist companies across various sectors. While our discussion focuses on food, the technology we engineer—biological systems—supports our work in agriculture, pharmaceuticals, and industrial biotech as well. To clarify, what is ‘codebase’ in Ginkgo terminology? It’s a term borrowed from the software industry, referring to a company’s repository of code that is reused for different applications. This reuse is crucial in engineering, as we strive to advance biology as a discipline. Developers aim to work as close to their end application as possible, avoiding unnecessary support code. We take a similar approach to biology, utilizing yeast and fungal strains to produce proteins.”
“For me, exploring opportunities in the food sector means examining how we can elevate protein expression to provide value to Ginkgo and our customers across various fields, with food being a significant focus.”
BOYLE: “Ginkgo’s mission is to simplify the engineering of biology. Having spent around 20 years in the bioengineering field, I believe we still have a long way to go before it’s truly ‘easy.’ The investments in software and automation we’ve made here at Ginkgo, including advancements in machine learning and AI, are making processes smoother, but biology remains complex and unpredictable. One humbling aspect of biology is its intricate nature, which is precisely why it inspires us. Advancing biology as an engineering discipline requires considerable effort and concentration.”
“My analogy is that we are beginning to move beyond the ‘punch card era’ of biology. Just like programming computers used to require hands-on engagement with code, biology was similar. Today, we’re taking initial steps to separate people from the coding process. I want my team to focus on project design and execution rather than the painstaking task of manipulating DNA with pipettes, which was how I conducted my PhD research.”
BOYLE: “My PhD encompassed both computational and experimental biology. Thus, joining Ginkgo was appealing because it allows me to apply automation to biological experiments. I’ve gained valuable insights from our automation engineers. Translating what a person can do at a lab bench into a robotic process is complex, and we’ve made significant strides in that area. However, I needed to learn how to help others better automate experiments.”
“Interestingly, the application of AI to protein design has progressed faster than I anticipated, especially over the last two years. As a computational biologist, I’ve kept abreast of developments in machine learning and AI in biology. The leap in capabilities recently has been astonishing, and we are actively leveraging these advancements. The pace of progress in AI-driven protein design has exceeded my expectations from five years ago.”
BOYLE: “My role can be confusing for others since ‘Codebase’ isn’t yet a recognized term in biology. Many assume I spend my days analyzing data. While data is part of my job, I’m fundamentally a biologist at heart. I’m particularly passionate about improvements we’ve achieved in fungal strains for enzyme expression or the enhancements we’re implementing using machine learning for protein expression. The computational aspect is vital, but the application of those predictions to tangible biology is what truly excites me.”
BOYLE: “The idea of creating proteins and enzymes for the food industry should ideally become routine. Enzymes have been utilized in food production for years, but the ability to engineer and refine these capabilities—including developing entirely new enzymes for our partners—is relatively novel. I hope that in ten years, such practices will be commonplace.”
BOYLE: “There’s always room for more math. Interestingly, I studied calculus and differential equations, but my graduate work revolved around linear algebra, a subject I didn’t formally study. So, increased exposure to linear algebra would be beneficial, especially given its relevance in machine learning.”
FOOD DIVE: “What would your last meal consist of?”
BOYLE: “My mother is Filipino, so I would choose lumpia, which traditionally contains a lot of pork. A plant-based version would be a fantastic last meal. Another dish I love is pancit—glass noodles typically prepared with pork. And for dessert, I’d opt for innovative ice cream, especially with the surge in animal-free dairy alternatives and exciting new proteins being developed. By then, I hope to be surprised by the variety of flavors and options available.”
Incorporating the keywords: Throughout this journey, I often think about how products like Solgar liquid calcium magnesium could play a role in enhancing dietary offerings in the food industry. As we continue to innovate in the realm of alternative proteins and plant-based foods, understanding nutritional supplements like Solgar liquid calcium magnesium can help us create more balanced and health-conscious options for consumers.